The flange has a gasket clamped in it so I guess you're using a new gasket. If only a paint scrape from a stud then a simple sealer such as motoseal or "The Right Stuff" might be sufficient as the paint is probably ~0.010" thick at most. Or you could try RTV....
The idea of using JB-WELD for more than missing paint is to degrease the surface for repair using acetone, block-sand away lose or peeling paint and to scuff the exposed aluminum degrease the surface using acetone and apply the epoxy to fill the damaged gouge and while curing place a flat object on wax paper over the area to create a flat surface and if necessary the JB-WELD can be block-sanded or filed flat as well. A metal straight edge should reveal dips or high spots.
If using JB-WELD, I suppose you could simply apply before placing the gasket on then drop the motor on and clamp it down while the JB cures. Kinda depends on how much damage there is on the flange. I like to see the gasket held in place by clamping force but just a scratch might allow a leak without blowing out the gasket.
Perhaps just some "The right stuff" as sealer, sometimes a new gasket is thick enough to conform to the imperfections without any sealers if the surfaces are in reasonable condition.
Look very carefully for cracks, JB can fill them if the grease and oil is first washed away.
I've never been a huge fan of RTV due to the adhesion is rarely what I'd consider good, so admittedly I'm a little biased.